I modified the files from CodeIgniter like explained by TaggedZi.
Then I added a new user library. Open Aptana 3 and navigate to:Window > Preferences > Aptana > Editors > PHP – Libraries
Click New user library, type in a name and select the path to the modified CodeIgniter library.

Adding a new user library for CodeIgniter 2

Deselect the library and close the Preferences.
Now open the properties of your actual project and go to PHP Buildpath > Libraries.Uncheck “Use Project specified settings”and select the CodeIgniter library.